gOpenMol

gOpenMol is a tool for the visualization and analysis of molecular structures and their chemical properties.

The home page is http://www.csc.fi/english/pages/g0penMol.
The manual is here: http://www.csc.fi/english/pages/g0penMol/tutorials/manual.pdf.

The current version is 3.00.
The files are in /home/bio/Gopenmol/gOpenMol-3.00.
You start the program by typing rungOpenMol

The program is very easy to use.

Left mouse button rotates the molecule
Middle mouse button rotates the molecule around Z axis
Right mouse button enlarge (up) or diminish (down) the molecule.

The only counter-intuitive feature is that you start to browse files from the last visited directory, not the one the program was started from.

Moreover, you need to rename the Turbomole coord file to coord.txt to be able to import it.

How to plot spin densities from Turbomole

  1. Insert into the control file:
    $pointval dens
  2. Run
    ridft -proper >logd
    This gives you the files coord.xyz and sd.plt (as well as td.plt = total density).
    More info for Turbomole here.
  3. rungOpenMol
  4. Import the coordinates from coord.xyz (File - Import - Coord - select file - Apply - Dissmiss).
  5. Import the spin density: Plot - Contour - Select sd.plt - Import - Select proper values for the contours
    (e.g. 0.005 - blue and -0.005 red)
    Apply and play with the contours
  6. Print to a file with
    File - Hardcopy
    Available formats are bmp, jpg, ps, rgb, tga, and xwd.
    PostScript works exelently.

How to edit some properties

  1. The background colour: Edit - Display Properties - Background colour
    or View - Background Colour - Colour
  2. Change the colour of an atom:
    View - Atom Colour - Enter the number of the atom as atom or atom name with capital letters (e.g. C for all carbons) and then select the colour
  3. Delete H atoms: Do it simply in the coord.xyz file by hand.
  4. Add or delete a bond: Edit - Molecule - Select atoms (by names) - create or break bond.
  5. View as sticks: View - Atom Type - Check licorice - Apply  (Cylinder and sphere radii 0.1 are appropriate)
  6. View as ball and stick: View - Atom Type - Check CPK - Apply
  7. Trun off ball or sticks: View - Atom Type - Check CPK - Check Off - Apply
  8. Change the colour of an atom: View - Atom Colours - Select an atom (by name) - Select a colour - Apply

Installation

The installation was trivial: unzip and untar. Then go to the gopenmol directory and run ./Install.
The only needed change was to
chmod-R  +r *

UR 27/9-07